Repositories list

• Bioinformatics-Translator-Queries

  Public
  Translator queries relevant to the Bioinformatics Core

  0•0•3•0•Updated Dec 23, 2024Dec 23, 2024

• Interactive-Enrichment-Analysis

  Public
  A set of Shiny apps to provide interactive enrichment analysis and exploration of results.

  bioinformaticsshinyfoss+ 2openscienceenrichment-analysis

  R

  •7•27•11•0•Updated Dec 15, 2024Dec 15, 2024

• Bioinformatics-Workshops

  Public
  Workshops presented by the Gladstone Bioinformatics Core

  HTML

  •62•187•10•0•Updated Dec 4, 2024Dec 4, 2024

• scRNA-seq_shiny_app_dashboard

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• RMeDPower2

  Public
  Helping design and analyses of data from repeated measures experiments

  HTML

  •0•1•0•0•Updated Feb 10, 2024Feb 10, 2024

• r_docker

  Public
  Docker container for genomics analyses in R.

  R

  •

  MIT License

  •7•0•0•0•Updated Dec 13, 2023Dec 13, 2023

• C3_R_Bootcamp_Bonus_Day

  Public
  Slides and materials for the last day of the C3 R bootcamp with topics chosen by the students

  CSS

  •0•0•0•0•Updated Nov 9, 2023Nov 9, 2023

• YH_MN01_NatureNeuroscience_paper

  Public
  single-nucleus RNA-seq analysis (15 samples)

  R

  •

  MIT License

  •0•0•1•0•Updated Sep 21, 2023Sep 21, 2023

• annotate-genes

  Public
  Filter GO annotations for a list of genes using mygene.info via R

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 15, 2023Sep 15, 2023

• RMeDPower

  Public
  R

  •0•1•0•0•Updated Aug 14, 2023Aug 14, 2023

• AlleleAnalyzer_bcft_RT

  Public
  A software tool for personalized and allele-specific CRISPR editing.

  Jupyter Notebook

  •

  MIT License

  •5•0•0•0•Updated Jan 3, 2023Jan 3, 2023

• PFOCRInPathwayAnalyses

  Public
  R

  •3•1•0•0•Updated Nov 22, 2021Nov 22, 2021

• Hota_et_al_2021_Brm_safeguards_canalization_cardiac_diff

  Public
  Shell

  •0•0•0•0•Updated Aug 6, 2021Aug 6, 2021

• GB-JL-1189-Jeremy-GEDI

  Public
  GEDI value cutoff threshold estimation

  HTML

  •0•0•0•0•Updated May 28, 2021May 28, 2021

• UCSCbrowserPy

  Public
  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 2, 2021Feb 2, 2021

• wynton-tutorials

  Public
  Legacy wynton documentation for reference

  JavaScript

  •1•0•0•0•Updated Nov 2, 2020Nov 2, 2020

• BC-TM-1123-KC

  Public
  Tamer Mohammed | scRNA-seq

  R

  •0•0•0•0•Updated Jun 18, 2020Jun 18, 2020

• MDC-971-KC

  Public
  HPV type identification

  Shell

  •0•0•0•0•Updated Jun 12, 2020Jun 12, 2020

• scRNA-seq_shiny_app

  Public
  R Shiny application for scRNA-seq

  R

  •0•1•0•0•Updated Apr 30, 2020Apr 30, 2020

• BC-AM-1148

  Public
  R Shiny application for scRNA-seq

  R

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 18, 2020Mar 18, 2020

• bioinformatics-r-functions

  Public
  Collection of generally useful R functions

  R

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 1, 2020Mar 1, 2020

• bioinformatics-datasets

  Public
  public datasets for testing, benchmarking and comparison

  R

  •1•0•0•0•Updated Feb 24, 2020Feb 24, 2020

• MonkeyPipeline

  Public
  Perl

  •1•0•13•0•Updated Jan 9, 2020Jan 9, 2020

• post-pipeline_RNA-seq_workshop

  Public
  RNA-seq workshop starting from a matrix of counts, with a **primary focus on linear modeling for differential expression**

  R

  •1•0•0•0•Updated May 17, 2019May 17, 2019

• stancon2018helsinki_intro

  Public
  StanCon2018 Helsinki Tutorial

  Stan

  •15•0•0•0•Updated Sep 3, 2018Sep 3, 2018

• knitr_case_studies

  Public
  Inference case studies in knitr

  HTML

  •97•0•0•0•Updated Apr 25, 2018Apr 25, 2018

• stancon2018_intro

  Public
  Materials for StanCon 2018 intro class

  Jupyter Notebook

  •9•0•0•0•Updated Feb 26, 2018Feb 26, 2018

• GI-bulk-RNAseq

  Public
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

  Groovy

  •

  MIT License

  •713•0•0•0•Updated Feb 1, 2018Feb 1, 2018

• git-flight-rules

  Public
  Flight rules for git

  Creative Commons Attribution Share Alike 4.0 International

  •3.2k•0•0•0•Updated Nov 10, 2017Nov 10, 2017

• awesome

  Public
  A curated list of resources that members of our group have found useful

  Apache License 2.0

  •1•1•0•0•Updated Aug 29, 2017Aug 29, 2017